Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi4g102 . . . . . . . . . . . . . Car12g00589 . . . . . . . . . . . . . . . . . . . . Cone20ag0270 . . . . . . . . Bpe14g00262 . . Bma02g00525 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1564 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g104 . Blo12g01014 . . . Bpe02g00488 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe02g00259 . . . . . . . . . . . . . . . . . .
Vvi4g105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g106 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g107 Blo01g01468 Blo12g01013 . . . . . . . . . . . . . . . . . . . . . . Cla05g01594 . . . . . . . . . Cone20ag0268 . . . . . . . . . . . . . Cmo01g01529 . . . . . . Cpe02g00257 . . . . . . . . . . . . . . . . . .
Vvi4g108 . Blo12g01012 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g109 . Blo12g01011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe02g00256 . . . . . . . . . . . . . . . . . .
Vvi4g110 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g111 . Blo12g01018 . Bda03g00138 . . Bma04g00122 . . . Cma01g01725 . Car09g00296 . . . Cpe06g00247 . . . . . . . Cla05g01845 . . Cco05g2041 . Cmu05g1843 . Cone4ag1674 Cone7ag1279 . . Lsi04g01414 . . . . . . . . Bpe04g00120 . . Sed11g1825 Cmo01g01788 Cmo09g00348 Cma09g00348 . Car01g01338 . . Cpe02g00271 Bhi09g03133 Tan01g4607 Cmetu07g2154 . Hepe01g1897 Mch11g0428 . . . . . . . . . . . Cme07g00210
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 1193200 1197254 + Bda016079.1 Bda03g00138 138
9 80320360 80325759 + XM_039043836.1 Bhi09g03133 3133
1 53894919 53907138 + BLOR01468 Blo01g01468 1468
12 28070107 28070937 - BLOR05030 Blo12g01011 1011
12 28072380 28074117 - BLOR05031 Blo12g01012 1012
12 28074927 28081473 - BLOR05032 Blo12g01013 1013
12 28084532 28085731 - BLOR05033 Blo12g01014 1014
12 28126110 28130158 - BLOR05037 Blo12g01018 1018
2 10458428 10460413 - Bma015028.1 Bma02g00525 525
4 972447 976496 + Bma018570.1 Bma04g00122 122
2 3163215 3163951 - Bpe008327.1 Bpe02g00488 488
4 822373 827531 + Bpe014841.2 Bpe04g00120 120
14 2721292 2722470 - Bpe006916.1 Bpe14g00262 262
1 11900432 11905268 + Carg10699-RA Car01g01338 1338
9 1661530 1671791 - Carg02775-RA Car09g00296 296
12 3928794 3929993 - Carg23958-RA Car12g00589 589
5 29480910 29492072 - CcPI632755_05g020410.1 Cco05g2041 2041
5 27021993 27028198 - ClCG05G015380.2 Cla05g01594 1594
5 30341092 30352693 - ClCG05G018010.2 Cla05g01845 1845
1 11692416 11698486 + CmaCh01G017250.1 Cma01g01725 1725
9 1443218 1448901 - CmaCh09G003480.1 Cma09g00348 348
7 1388242 1393938 + MELO3C016885.2.1 Cme07g00210 210
7 23418626 23423845 - PI0028193.1 Cmetu07g2154 2154
1 11809003 11817549 + CmoCh01G015290.1 Cmo01g01529 1529
1 13189717 13195716 - CmoCh01G017880.1 Cmo01g01788 1788
9 1505917 1510988 - CmoCh09G003480.1 Cmo09g00348 348
5 28488688 28500108 - CmPI595203_05g018430.1 Cmu05g1843 1843
4 12527374 12531790 - Conep04aG0172800.1 Cone4ag1674 1674
7 9466573 9470257 + Conep07aG0131700.1 Cone7ag1279 1279
7 10740700 10744052 - Conep07aG0161000.1 Cone7ag1564 1564
20 1188315 1190335 + Conep20aG0027800.1 Cone20ag0267 267
20 1190376 1195243 - Conep20aG0027900.1 Cone20ag0268 268
20 1203835 1206176 - Conep20aG0028100.1 Cone20ag0270 270
2 1318888 1329507 - Cp4.1LG02g06210.1 Cpe02g00256 256
2 1330695 1337874 - Cp4.1LG02g06190.1 Cpe02g00257 257
2 1342721 1345432 - Cp4.1LG02g06040.1 Cpe02g00259 259
2 1402807 1408692 - Cp4.1LG02g06050.1 Cpe02g00271 271
6 1316283 1326461 - Cp4.1LG06g02570.1 Cpe06g00247 247
1 83808806 83813725 - Hsped.01g18970.1 Hepe01g1897 1897
4 21900042 21911052 + Lsi04G014140.1 Lsi04g01414 1414
11 2686429 2691740 - MC11g0345 Mch11g0428 428
11 33063700 33069138 + Sed0005137.2 Sed11g1825 1825
1 112047002 112051708 + Tan0022407.1 Tan01g4607 4607
4 1036987 1039484 + Vvi4g102 Vvi4g102 102
4 1044793 1048906 + Vvi4g103 Vvi4g103 103
4 1062804 1064236 + Vvi4g104 Vvi4g104 104
4 1067343 1068214 + Vvi4g105 Vvi4g105 105
4 1068283 1074131 + Vvi4g106 Vvi4g106 106
4 1079722 1090460 + Vvi4g107 Vvi4g107 107
4 1090827 1092862 + Vvi4g108 Vvi4g108 108
4 1094384 1098549 + Vvi4g109 Vvi4g109 109
4 1099193 1103857 - Vvi4g110 Vvi4g110 110
4 1104424 1110865 - Vvi4g111 Vvi4g111 111
       

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